Bag of Tricks for Node Classification with Graph Neural Networks
Abstract
Over the past few years, graph neural networks (GNN) and label propagation-based methods have made significant progress in addressing node classification tasks on graphs. However, in addition to their reliance on elaborate architectures and algorithms, there are several key technical details that are frequently overlooked, and yet nonetheless can play a vital role in achieving satisfactory performance. In this paper, we first summarize a series of existing tricks-of-the-trade, and then propose several new ones related to label usage,. loss function formulation, and model design that can significantly improve various GNN architectures. We empirically evaluate their impact on final node classification accuracy by conducting ablation studies and demonstrate consistently-improved performance, often to an extent that outweighs the gains from more dramatic changes in the underlying GNN architecture. Notably, many of the top-ranked models on the Open Graph Benchmark (OGB) leaderboard and KDDCUP 2021 Large-Scale Challenge MAG240M-LSC benefit from these techniques we initiated.
Benchmark Results
Tested on 4 datasets 1 baseline value reported too low Non-standard metric on 1 dataset
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels (2017) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 | |
| 44 | GAT | 0.8897
±0.0014 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 325 | GAT+norm.adj. | 0.8372
±0.0074 | This paper |
| 724 | MLP | 0.7768 best reported | best at pub: Adversarial Graph Disentanglement with Component-specific Aggregation (2021) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 350 | MLP | 0.7289
±0.0010 best reported | best at pub: Adversarial Graph Disentanglement with Component-specific Aggregation (2021) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 437 | GAT+norm.adj. | 0.7225
±0.0104 | This paper |
| 463 | vanilla GAT | 0.7192
±0.0092 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 210 | MLP | 0.8690
±0.0074 best reported | best at pub: Adversarial Graph Disentanglement with Component-specific Aggregation (2021) best today: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) |
| 623 | GAT+norm.adj. | 0.7877
±0.0054 | This paper |
| 646 | vanilla GAT | 0.7843
±0.0064 | This paper |
Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GAP-EDP | 0.9870
±0.0003 | |
| 2 | NE-ASGCN | 0.9758
±0.0027 | |
| 3 | HSGT | 0.9730
±0.0024 | |
| 5 | GAT+norm.adj. | 0.9706
±0.0005 | This paper |
| 8 | vanilla GAT | 0.9697
±0.0004 | This paper |
| 21 | GraphSAGE | 0.9653
±0.0011 | |
| 26 | GCN | 0.9648 best reported | best at pub: DropEdge: Towards Deep Graph Convolutional Networks on Node Classification (ICLR 2019) |
| 147 | MLP | 0.8240
±0.0010 best reported |
